MuscleExample: Subset of Inflammatory Myopathy Dataset to Demonstrate...

In sigPathway: Pathway Analysis

Description

MuscleExample is an R workspace containing the following objects: (1) tab: a matrix of 5000 rows and 15 columns (2) phenotype: a indicator vector which denotes which columns in tab are arrays from normal (NORM) and inclusion body myositis (IBM) (3) G: a list containing the source, title, and the probe set IDs associated with 626 pathways

The full inflammatory myopathway dataset (which includes all probe sets and samples, including more NORM, IBM, and dermatomyositis arrays) and a more comprehensive pathway annotation list for the HG-U133A and other selected array platforms are available at http://www.chip.org/~ppark/PNAS05/

Although the objects contained in MuscleExample are subsets of the full dataset, the results obtained from running pathway analysis with MuscleExample are comparable to those obtained using the full dataset. This example dataset contains 8 IBM and 7 NORM arrays. The 5000 probe sets were selected by considering the variance of the expression values of each probe set among the 15 arrays.

Usage

data(MuscleExample)

Format

1 integer matrix, 1 numeric vector, and 1 list

Source

http://www.chip.org/~ppark/PNAS05/

References

Tian L., Greenberg S.A., Kong S.W., Altschuler J., Kohane I.S., Park P.J. (2005) Discovering statistically significant pathways in expression profiling studies. Proceedings of the National Academy of Sciences of the USA, 102, 13544-9.

http://www.pnas.org/cgi/doi/10.1073/pnas.0506577102

sigPathway documentation built on Nov. 8, 2020, 5:35 p.m.